The Robins took the lead through Jonathan Stead but Reading came back with first-half goals from Jobi McAnuff and Noel Hunt, followed by a masterful brace from Shane Long after the break.
Millen said: "I don't want to make excuses but we have had the flu bug round the ground this week and training has been disrupted because we couldn't get onto the grass.
"But it was more the team performance and some individual errors that have let Reading in today.
"Albert Adomah has apologised to the lads for the mistake that allowed (Hunt) to score their second goal and take the lead, but he is a young lad and will learn from that.
"(Long) was terrific. He doesn't stop working and running and if you constantly run into the right areas as he does the chances will fall to you."
Source: PA
Source: PA